The shape and position of the medieval, probably 12thc., chancel is indicated by the scarring on the outside face of the east wall of the nave. To the north of the north wall of the chancel is a ragged joint which is approximately in line with the end of the roof line. In the east wall of the nave, to the south of the present south wall of the chancel, the end of the former chancel's roof line is clear. Beneath the end of this line there are indications of some disturbance in the masonry, though it is markedly less clear than on the north side of the chancel. The nave has been widened to the south. A Perpendicular tower was added at the west end.

The only Romanesque carvings in situ are the impost blocks of the chancel arch, but there are some loose fragments in the church.

The manor of Alton Priors was the property of the Bishops of Winchester, which was valued in 1086 as £29. In 1290 the church was described as a chapel annexed to the parish of Overton, but before this it appears to have been an independent rectory.